I don't know that there's really much to this, but Martin Van Buren Bates, a Confederate Soldier who was said to be 2.36 m tall, married Anna Haining Swan, a Canadian woman who was 2.27 m tall. They later conceived a child who was 86.4 cm long and weighed approximately 10.5 kilos at birth, but the child died 11 hours later due to difficulty in labor.

Neither of them seemed to suffer any kind of pathological condition which caused their height, nor from any health conditions directly linked to their height (Anna's case is debatable).

Do you think that some kind of nearly extinct species of giants (really just a sub-group of humans) could have been destroyed at some point in human history, and the Foundation saw it as keeping in human interests to prevent them from breeding?

The problem here is that you are trying to use a real life event as the bulk of your story and really not adding too much to it. The fact that you are trying to explain a real life (minor) tragedy as "Foundation did it" seems a bit tasteless.